Starting phenix.real_space_refine on Wed Feb 12 07:09:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5h1b_9566/02_2025/5h1b_9566.cif Found real_map, /net/cci-nas-00/data/ceres_data/5h1b_9566/02_2025/5h1b_9566.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/5h1b_9566/02_2025/5h1b_9566.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5h1b_9566/02_2025/5h1b_9566.map" model { file = "/net/cci-nas-00/data/ceres_data/5h1b_9566/02_2025/5h1b_9566.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5h1b_9566/02_2025/5h1b_9566.cif" } resolution = 4.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 18 5.49 5 Mg 3 5.21 5 S 39 5.16 5 C 4557 2.51 5 N 1287 2.21 5 O 1455 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 7359 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2361 Number of conformers: 1 Conformer: "" Number of residues, atoms: 308, 2361 Classifications: {'peptide': 308} Link IDs: {'CIS': 2, 'PTRANS': 9, 'TRANS': 296} Chain breaks: 1 Chain: "D" Number of atoms: 180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 180 Classifications: {'DNA': 9} Link IDs: {'rna3p': 8} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Restraints were copied for chains: B, C Time building chain proxies: 4.58, per 1000 atoms: 0.62 Number of scatterers: 7359 At special positions: 0 Unit cell: (107.092, 69.218, 116.234, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 39 16.00 P 18 15.00 Mg 3 11.99 O 1455 8.00 N 1287 7.00 C 4557 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.05 Conformation dependent library (CDL) restraints added in 998.2 milliseconds 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1686 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 6 sheets defined 54.1% alpha, 12.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.02 Creating SS restraints... Processing helix chain 'A' and resid 24 through 28 Processing helix chain 'A' and resid 34 through 45 removed outlier: 3.792A pdb=" N VAL A 38 " --> pdb=" O ASN A 34 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLU A 43 " --> pdb=" O LYS A 39 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLY A 45 " --> pdb=" O LEU A 41 " (cutoff:3.500A) Processing helix chain 'A' and resid 48 through 54 removed outlier: 4.068A pdb=" N VAL A 52 " --> pdb=" O THR A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 62 Processing helix chain 'A' and resid 67 through 82 Processing helix chain 'A' and resid 88 through 99 Processing helix chain 'A' and resid 106 through 113 Processing helix chain 'A' and resid 132 through 144 Processing helix chain 'A' and resid 145 through 146 No H-bonds generated for 'chain 'A' and resid 145 through 146' Processing helix chain 'A' and resid 147 through 151 Processing helix chain 'A' and resid 167 through 179 Processing helix chain 'A' and resid 181 through 188 removed outlier: 3.717A pdb=" N ASN A 188 " --> pdb=" O ASP A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 214 removed outlier: 3.768A pdb=" N THR A 201 " --> pdb=" O THR A 197 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLN A 202 " --> pdb=" O ASP A 198 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N GLU A 213 " --> pdb=" O ALA A 209 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N SER A 214 " --> pdb=" O MET A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 232 removed outlier: 3.974A pdb=" N ARG A 229 " --> pdb=" O THR A 225 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N THR A 230 " --> pdb=" O ALA A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 260 removed outlier: 3.602A pdb=" N ARG A 247 " --> pdb=" O MET A 243 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N MET A 251 " --> pdb=" O ARG A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 296 removed outlier: 3.804A pdb=" N ILE A 292 " --> pdb=" O GLY A 288 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ALA A 295 " --> pdb=" O ILE A 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 28 Processing helix chain 'B' and resid 34 through 45 removed outlier: 3.792A pdb=" N VAL B 38 " --> pdb=" O ASN B 34 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLU B 43 " --> pdb=" O LYS B 39 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLY B 45 " --> pdb=" O LEU B 41 " (cutoff:3.500A) Processing helix chain 'B' and resid 48 through 54 removed outlier: 4.068A pdb=" N VAL B 52 " --> pdb=" O THR B 48 " (cutoff:3.500A) Processing helix chain 'B' and resid 56 through 62 Processing helix chain 'B' and resid 67 through 82 Processing helix chain 'B' and resid 89 through 99 Processing helix chain 'B' and resid 106 through 113 Processing helix chain 'B' and resid 132 through 144 Processing helix chain 'B' and resid 145 through 146 No H-bonds generated for 'chain 'B' and resid 145 through 146' Processing helix chain 'B' and resid 147 through 151 Processing helix chain 'B' and resid 167 through 179 Processing helix chain 'B' and resid 181 through 188 removed outlier: 3.716A pdb=" N ASN B 188 " --> pdb=" O ASP B 184 " (cutoff:3.500A) Processing helix chain 'B' and resid 196 through 214 removed outlier: 3.768A pdb=" N THR B 201 " --> pdb=" O THR B 197 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLN B 202 " --> pdb=" O ASP B 198 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N GLU B 213 " --> pdb=" O ALA B 209 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N SER B 214 " --> pdb=" O MET B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 225 through 232 removed outlier: 3.974A pdb=" N ARG B 229 " --> pdb=" O THR B 225 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N THR B 230 " --> pdb=" O ALA B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 260 removed outlier: 3.602A pdb=" N ARG B 247 " --> pdb=" O MET B 243 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N MET B 251 " --> pdb=" O ARG B 247 " (cutoff:3.500A) Processing helix chain 'B' and resid 288 through 296 removed outlier: 3.804A pdb=" N ILE B 292 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ALA B 295 " --> pdb=" O ILE B 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 24 through 28 Processing helix chain 'C' and resid 34 through 45 removed outlier: 3.792A pdb=" N VAL C 38 " --> pdb=" O ASN C 34 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLU C 43 " --> pdb=" O LYS C 39 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLY C 45 " --> pdb=" O LEU C 41 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 54 removed outlier: 4.067A pdb=" N VAL C 52 " --> pdb=" O THR C 48 " (cutoff:3.500A) Processing helix chain 'C' and resid 56 through 62 Processing helix chain 'C' and resid 67 through 82 Processing helix chain 'C' and resid 88 through 99 Processing helix chain 'C' and resid 106 through 113 Processing helix chain 'C' and resid 132 through 144 Processing helix chain 'C' and resid 145 through 146 No H-bonds generated for 'chain 'C' and resid 145 through 146' Processing helix chain 'C' and resid 147 through 151 Processing helix chain 'C' and resid 167 through 179 Processing helix chain 'C' and resid 181 through 188 removed outlier: 3.716A pdb=" N ASN C 188 " --> pdb=" O ASP C 184 " (cutoff:3.500A) Processing helix chain 'C' and resid 196 through 214 removed outlier: 3.768A pdb=" N THR C 201 " --> pdb=" O THR C 197 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLN C 202 " --> pdb=" O ASP C 198 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N GLU C 213 " --> pdb=" O ALA C 209 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N SER C 214 " --> pdb=" O MET C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 225 through 232 removed outlier: 3.973A pdb=" N ARG C 229 " --> pdb=" O THR C 225 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N THR C 230 " --> pdb=" O ALA C 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 238 through 260 removed outlier: 3.602A pdb=" N ARG C 247 " --> pdb=" O MET C 243 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N MET C 251 " --> pdb=" O ARG C 247 " (cutoff:3.500A) Processing helix chain 'C' and resid 288 through 296 removed outlier: 3.804A pdb=" N ILE C 292 " --> pdb=" O GLY C 288 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ALA C 295 " --> pdb=" O ILE C 291 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 324 through 327 removed outlier: 8.173A pdb=" N LEU A 300 " --> pdb=" O ILE A 122 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N GLU A 124 " --> pdb=" O LEU A 300 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N LEU A 302 " --> pdb=" O GLU A 124 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N PHE A 126 " --> pdb=" O LEU A 302 " (cutoff:3.500A) removed outlier: 7.934A pdb=" N LYS A 304 " --> pdb=" O PHE A 126 " (cutoff:3.500A) removed outlier: 5.859A pdb=" N THR A 123 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N ASN A 267 " --> pdb=" O THR A 123 " (cutoff:3.500A) removed outlier: 5.908A pdb=" N MET A 125 " --> pdb=" O ASN A 267 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N LYS A 156 " --> pdb=" O ALA A 217 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N LEU A 219 " --> pdb=" O LYS A 156 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N MET A 158 " --> pdb=" O LEU A 219 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N VAL A 221 " --> pdb=" O MET A 158 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N ILE A 160 " --> pdb=" O VAL A 221 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALA A 192 " --> pdb=" O TYR A 159 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ASP A 161 " --> pdb=" O ALA A 192 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 329 through 330 Processing sheet with id=AA3, first strand: chain 'B' and resid 190 through 193 removed outlier: 3.717A pdb=" N ALA B 192 " --> pdb=" O TYR B 159 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ASP B 161 " --> pdb=" O ALA B 192 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N LYS B 156 " --> pdb=" O ALA B 217 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N LEU B 219 " --> pdb=" O LYS B 156 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N MET B 158 " --> pdb=" O LEU B 219 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N VAL B 221 " --> pdb=" O MET B 158 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N ILE B 160 " --> pdb=" O VAL B 221 " (cutoff:3.500A) removed outlier: 5.859A pdb=" N THR B 123 " --> pdb=" O ILE B 265 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N ASN B 267 " --> pdb=" O THR B 123 " (cutoff:3.500A) removed outlier: 5.908A pdb=" N MET B 125 " --> pdb=" O ASN B 267 " (cutoff:3.500A) removed outlier: 8.173A pdb=" N LEU B 300 " --> pdb=" O ILE B 122 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N GLU B 124 " --> pdb=" O LEU B 300 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N LEU B 302 " --> pdb=" O GLU B 124 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N PHE B 126 " --> pdb=" O LEU B 302 " (cutoff:3.500A) removed outlier: 7.934A pdb=" N LYS B 304 " --> pdb=" O PHE B 126 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 329 through 330 Processing sheet with id=AA5, first strand: chain 'C' and resid 190 through 193 removed outlier: 3.717A pdb=" N ALA C 192 " --> pdb=" O TYR C 159 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ASP C 161 " --> pdb=" O ALA C 192 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N LYS C 156 " --> pdb=" O ALA C 217 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N LEU C 219 " --> pdb=" O LYS C 156 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N MET C 158 " --> pdb=" O LEU C 219 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N VAL C 221 " --> pdb=" O MET C 158 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N ILE C 160 " --> pdb=" O VAL C 221 " (cutoff:3.500A) removed outlier: 5.859A pdb=" N THR C 123 " --> pdb=" O ILE C 265 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N ASN C 267 " --> pdb=" O THR C 123 " (cutoff:3.500A) removed outlier: 5.909A pdb=" N MET C 125 " --> pdb=" O ASN C 267 " (cutoff:3.500A) removed outlier: 8.174A pdb=" N LEU C 300 " --> pdb=" O ILE C 122 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N GLU C 124 " --> pdb=" O LEU C 300 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N LEU C 302 " --> pdb=" O GLU C 124 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N PHE C 126 " --> pdb=" O LEU C 302 " (cutoff:3.500A) removed outlier: 7.934A pdb=" N LYS C 304 " --> pdb=" O PHE C 126 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 329 through 330 334 hydrogen bonds defined for protein. 918 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.16 Time building geometry restraints manager: 2.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2372 1.33 - 1.45: 1159 1.45 - 1.57: 3854 1.57 - 1.69: 33 1.69 - 1.81: 63 Bond restraints: 7481 Sorted by residual: bond pdb=" O3A ANP A 600 " pdb=" PB ANP A 600 " ideal model delta sigma weight residual 1.700 1.550 0.150 2.00e-02 2.50e+03 5.65e+01 bond pdb=" O3A ANP B 600 " pdb=" PB ANP B 600 " ideal model delta sigma weight residual 1.700 1.550 0.150 2.00e-02 2.50e+03 5.63e+01 bond pdb=" O3A ANP C 600 " pdb=" PB ANP C 600 " ideal model delta sigma weight residual 1.700 1.550 0.150 2.00e-02 2.50e+03 5.60e+01 bond pdb=" N3B ANP C 600 " pdb=" PG ANP C 600 " ideal model delta sigma weight residual 1.795 1.689 0.106 2.00e-02 2.50e+03 2.82e+01 bond pdb=" N3B ANP A 600 " pdb=" PG ANP A 600 " ideal model delta sigma weight residual 1.795 1.689 0.106 2.00e-02 2.50e+03 2.80e+01 ... (remaining 7476 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.75: 9923 3.75 - 7.51: 204 7.51 - 11.26: 15 11.26 - 15.01: 0 15.01 - 18.77: 3 Bond angle restraints: 10145 Sorted by residual: angle pdb=" PB ANP C 600 " pdb=" N3B ANP C 600 " pdb=" PG ANP C 600 " ideal model delta sigma weight residual 126.95 108.18 18.77 3.00e+00 1.11e-01 3.91e+01 angle pdb=" PB ANP B 600 " pdb=" N3B ANP B 600 " pdb=" PG ANP B 600 " ideal model delta sigma weight residual 126.95 108.18 18.77 3.00e+00 1.11e-01 3.91e+01 angle pdb=" PB ANP A 600 " pdb=" N3B ANP A 600 " pdb=" PG ANP A 600 " ideal model delta sigma weight residual 126.95 108.20 18.75 3.00e+00 1.11e-01 3.91e+01 angle pdb=" N THR A 197 " pdb=" CA THR A 197 " pdb=" C THR A 197 " ideal model delta sigma weight residual 111.71 105.46 6.25 1.15e+00 7.56e-01 2.95e+01 angle pdb=" N THR B 197 " pdb=" CA THR B 197 " pdb=" C THR B 197 " ideal model delta sigma weight residual 111.71 105.47 6.24 1.15e+00 7.56e-01 2.94e+01 ... (remaining 10140 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.74: 4322 23.74 - 47.48: 162 47.48 - 71.22: 46 71.22 - 94.96: 27 94.96 - 118.70: 3 Dihedral angle restraints: 4560 sinusoidal: 1926 harmonic: 2634 Sorted by residual: dihedral pdb=" CA CYS C 319 " pdb=" C CYS C 319 " pdb=" N LEU C 320 " pdb=" CA LEU C 320 " ideal model delta harmonic sigma weight residual 180.00 -156.98 -23.02 0 5.00e+00 4.00e-02 2.12e+01 dihedral pdb=" CA CYS B 319 " pdb=" C CYS B 319 " pdb=" N LEU B 320 " pdb=" CA LEU B 320 " ideal model delta harmonic sigma weight residual -180.00 -156.98 -23.02 0 5.00e+00 4.00e-02 2.12e+01 dihedral pdb=" CA CYS A 319 " pdb=" C CYS A 319 " pdb=" N LEU A 320 " pdb=" CA LEU A 320 " ideal model delta harmonic sigma weight residual 180.00 -156.99 -23.01 0 5.00e+00 4.00e-02 2.12e+01 ... (remaining 4557 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 888 0.064 - 0.129: 244 0.129 - 0.193: 23 0.193 - 0.257: 0 0.257 - 0.321: 3 Chirality restraints: 1158 Sorted by residual: chirality pdb=" C3' ANP C 600 " pdb=" C2' ANP C 600 " pdb=" C4' ANP C 600 " pdb=" O3' ANP C 600 " both_signs ideal model delta sigma weight residual False -2.36 -2.68 0.32 2.00e-01 2.50e+01 2.58e+00 chirality pdb=" C3' ANP B 600 " pdb=" C2' ANP B 600 " pdb=" C4' ANP B 600 " pdb=" O3' ANP B 600 " both_signs ideal model delta sigma weight residual False -2.36 -2.68 0.32 2.00e-01 2.50e+01 2.56e+00 chirality pdb=" C3' ANP A 600 " pdb=" C2' ANP A 600 " pdb=" C4' ANP A 600 " pdb=" O3' ANP A 600 " both_signs ideal model delta sigma weight residual False -2.36 -2.67 0.32 2.00e-01 2.50e+01 2.50e+00 ... (remaining 1155 not shown) Planarity restraints: 1272 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA A 246 " -0.011 2.00e-02 2.50e+03 2.27e-02 5.15e+00 pdb=" C ALA A 246 " 0.039 2.00e-02 2.50e+03 pdb=" O ALA A 246 " -0.015 2.00e-02 2.50e+03 pdb=" N ARG A 247 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA B 246 " -0.011 2.00e-02 2.50e+03 2.25e-02 5.06e+00 pdb=" C ALA B 246 " 0.039 2.00e-02 2.50e+03 pdb=" O ALA B 246 " -0.015 2.00e-02 2.50e+03 pdb=" N ARG B 247 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA C 246 " -0.011 2.00e-02 2.50e+03 2.24e-02 5.00e+00 pdb=" C ALA C 246 " 0.039 2.00e-02 2.50e+03 pdb=" O ALA C 246 " -0.015 2.00e-02 2.50e+03 pdb=" N ARG C 247 " -0.013 2.00e-02 2.50e+03 ... (remaining 1269 not shown) Histogram of nonbonded interaction distances: 1.50 - 2.18: 46 2.18 - 2.86: 3020 2.86 - 3.54: 11307 3.54 - 4.22: 18610 4.22 - 4.90: 29872 Nonbonded interactions: 62855 Sorted by model distance: nonbonded pdb=" CB ALA A 271 " pdb=" OP2 DT D 4 " model vdw 1.503 3.460 nonbonded pdb=" CA ALA A 271 " pdb=" OP2 DT D 4 " model vdw 1.572 3.470 nonbonded pdb=" N ALA A 271 " pdb=" OP2 DT D 4 " model vdw 1.580 3.120 nonbonded pdb=" OH TYR B 159 " pdb=" OD2 ASP B 222 " model vdw 1.586 3.040 nonbonded pdb=" OH TYR A 159 " pdb=" OD2 ASP A 222 " model vdw 1.586 3.040 ... (remaining 62850 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.520 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.250 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 20.860 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7180 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.150 7481 Z= 0.667 Angle : 1.411 18.767 10145 Z= 0.917 Chirality : 0.056 0.321 1158 Planarity : 0.005 0.034 1272 Dihedral : 16.126 118.695 2874 Min Nonbonded Distance : 1.503 Molprobity Statistics. All-atom Clashscore : 54.25 Ramachandran Plot: Outliers : 2.63 % Allowed : 6.25 % Favored : 91.12 % Rotamer: Outliers : 5.67 % Allowed : 2.43 % Favored : 91.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.67 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.51 (0.27), residues: 912 helix: -2.43 (0.18), residues: 378 sheet: -0.80 (0.40), residues: 159 loop : 0.92 (0.36), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.002 HIS C 138 PHE 0.018 0.003 PHE C 86 TYR 0.019 0.002 TYR A 315 ARG 0.010 0.002 ARG C 215 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 98 time to evaluate : 0.880 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 ILE cc_start: 0.6707 (OUTLIER) cc_final: 0.6302 (mp) REVERT: A 265 ILE cc_start: 0.8748 (OUTLIER) cc_final: 0.8424 (mm) REVERT: B 62 ASN cc_start: 0.7700 (m-40) cc_final: 0.7444 (m110) REVERT: B 99 ILE cc_start: 0.6839 (OUTLIER) cc_final: 0.6453 (mp) REVERT: B 170 ARG cc_start: 0.7633 (OUTLIER) cc_final: 0.6648 (mpt180) REVERT: B 265 ILE cc_start: 0.8682 (OUTLIER) cc_final: 0.8012 (mm) outliers start: 42 outliers final: 13 residues processed: 132 average time/residue: 0.3011 time to fit residues: 48.6848 Evaluate side-chains 72 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 54 time to evaluate : 0.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 75 optimal weight: 7.9990 chunk 68 optimal weight: 5.9990 chunk 37 optimal weight: 9.9990 chunk 23 optimal weight: 1.9990 chunk 46 optimal weight: 8.9990 chunk 36 optimal weight: 6.9990 chunk 70 optimal weight: 3.9990 chunk 27 optimal weight: 20.0000 chunk 42 optimal weight: 5.9990 chunk 52 optimal weight: 1.9990 chunk 81 optimal weight: 3.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 ASN A 138 HIS ** A 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 138 HIS ** B 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 93 HIS C 138 HIS ** C 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.040395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2723 r_free = 0.2723 target = 0.034835 restraints weight = 51830.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2763 r_free = 0.2763 target = 0.035927 restraints weight = 29022.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.2792 r_free = 0.2792 target = 0.036719 restraints weight = 18534.936| |-----------------------------------------------------------------------------| r_work (final): 0.2787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.4034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 7481 Z= 0.287 Angle : 0.777 7.710 10145 Z= 0.412 Chirality : 0.044 0.167 1158 Planarity : 0.005 0.042 1272 Dihedral : 13.507 111.171 1191 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 18.10 Ramachandran Plot: Outliers : 1.32 % Allowed : 4.28 % Favored : 94.41 % Rotamer: Outliers : 0.54 % Allowed : 0.94 % Favored : 98.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.67 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.27), residues: 912 helix: -0.30 (0.23), residues: 429 sheet: -0.58 (0.40), residues: 168 loop : 0.45 (0.37), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS B 294 PHE 0.019 0.002 PHE B 126 TYR 0.018 0.002 TYR B 315 ARG 0.007 0.001 ARG B 193 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 68 time to evaluate : 0.910 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 ASN cc_start: 0.8741 (m-40) cc_final: 0.8371 (m110) REVERT: A 99 ILE cc_start: 0.8041 (OUTLIER) cc_final: 0.7839 (mt) REVERT: A 137 CYS cc_start: 0.9000 (m) cc_final: 0.8758 (m) REVERT: B 62 ASN cc_start: 0.8763 (m-40) cc_final: 0.8351 (m110) REVERT: B 248 PHE cc_start: 0.9343 (t80) cc_final: 0.9028 (t80) REVERT: B 251 MET cc_start: 0.9170 (tpt) cc_final: 0.8902 (tpt) REVERT: C 62 ASN cc_start: 0.8752 (m-40) cc_final: 0.8365 (p0) REVERT: C 210 MET cc_start: 0.8094 (mtt) cc_final: 0.7868 (mtt) REVERT: C 251 MET cc_start: 0.9141 (tpt) cc_final: 0.8521 (tpt) REVERT: C 301 TYR cc_start: 0.8916 (t80) cc_final: 0.8690 (t80) outliers start: 4 outliers final: 0 residues processed: 72 average time/residue: 0.2242 time to fit residues: 21.6880 Evaluate side-chains 46 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 45 time to evaluate : 0.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 58 optimal weight: 8.9990 chunk 21 optimal weight: 1.9990 chunk 34 optimal weight: 6.9990 chunk 53 optimal weight: 6.9990 chunk 24 optimal weight: 8.9990 chunk 77 optimal weight: 2.9990 chunk 46 optimal weight: 9.9990 chunk 76 optimal weight: 7.9990 chunk 7 optimal weight: 6.9990 chunk 74 optimal weight: 6.9990 chunk 23 optimal weight: 3.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 199 HIS C 267 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.038776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2667 r_free = 0.2667 target = 0.033673 restraints weight = 54863.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2707 r_free = 0.2707 target = 0.034714 restraints weight = 30417.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2734 r_free = 0.2734 target = 0.035439 restraints weight = 19283.983| |-----------------------------------------------------------------------------| r_work (final): 0.2735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.4999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 7481 Z= 0.315 Angle : 0.709 7.473 10145 Z= 0.376 Chirality : 0.042 0.171 1158 Planarity : 0.004 0.040 1272 Dihedral : 12.672 107.395 1191 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 16.88 Ramachandran Plot: Outliers : 1.32 % Allowed : 5.59 % Favored : 93.09 % Rotamer: Outliers : 0.27 % Allowed : 2.43 % Favored : 97.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.67 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.27), residues: 912 helix: 0.41 (0.23), residues: 447 sheet: -0.73 (0.39), residues: 168 loop : 0.02 (0.37), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 294 PHE 0.017 0.002 PHE B 86 TYR 0.023 0.002 TYR C 315 ARG 0.004 0.001 ARG B 193 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 56 time to evaluate : 0.899 Fit side-chains revert: symmetry clash REVERT: A 62 ASN cc_start: 0.8607 (m-40) cc_final: 0.8318 (p0) REVERT: A 137 CYS cc_start: 0.9003 (m) cc_final: 0.8730 (m) REVERT: A 251 MET cc_start: 0.9046 (tpt) cc_final: 0.8402 (tpt) REVERT: B 62 ASN cc_start: 0.8726 (m-40) cc_final: 0.8339 (m110) REVERT: B 137 CYS cc_start: 0.9225 (m) cc_final: 0.9013 (m) REVERT: B 225 THR cc_start: 0.9261 (p) cc_final: 0.8785 (p) REVERT: B 243 MET cc_start: 0.8553 (tmm) cc_final: 0.8288 (tmm) REVERT: C 62 ASN cc_start: 0.8827 (m-40) cc_final: 0.8492 (p0) REVERT: C 125 MET cc_start: 0.8397 (mmt) cc_final: 0.8163 (mmm) REVERT: C 137 CYS cc_start: 0.9201 (m) cc_final: 0.8960 (m) REVERT: C 206 GLN cc_start: 0.9103 (mt0) cc_final: 0.8730 (tt0) REVERT: C 251 MET cc_start: 0.9022 (tpt) cc_final: 0.8494 (tpt) outliers start: 2 outliers final: 0 residues processed: 58 average time/residue: 0.1716 time to fit residues: 14.7035 Evaluate side-chains 44 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 44 time to evaluate : 0.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 51 optimal weight: 7.9990 chunk 19 optimal weight: 6.9990 chunk 24 optimal weight: 10.0000 chunk 42 optimal weight: 8.9990 chunk 81 optimal weight: 8.9990 chunk 46 optimal weight: 8.9990 chunk 3 optimal weight: 0.2980 chunk 22 optimal weight: 10.0000 chunk 9 optimal weight: 0.6980 chunk 86 optimal weight: 0.9980 chunk 30 optimal weight: 10.0000 overall best weight: 3.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 242 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.039049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2676 r_free = 0.2676 target = 0.033756 restraints weight = 53578.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2717 r_free = 0.2717 target = 0.034840 restraints weight = 29786.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2745 r_free = 0.2745 target = 0.035600 restraints weight = 18866.346| |-----------------------------------------------------------------------------| r_work (final): 0.2742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.5496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 7481 Z= 0.244 Angle : 0.656 9.750 10145 Z= 0.346 Chirality : 0.040 0.166 1158 Planarity : 0.004 0.051 1272 Dihedral : 12.518 106.297 1191 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 14.76 Ramachandran Plot: Outliers : 1.21 % Allowed : 4.17 % Favored : 94.63 % Rotamer: Outliers : 0.13 % Allowed : 1.89 % Favored : 97.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.67 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.27), residues: 912 helix: 0.83 (0.24), residues: 447 sheet: -0.76 (0.38), residues: 168 loop : -0.00 (0.37), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 294 PHE 0.017 0.002 PHE B 86 TYR 0.017 0.001 TYR B 315 ARG 0.004 0.001 ARG B 193 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 58 time to evaluate : 0.786 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 LYS cc_start: 0.8835 (pttp) cc_final: 0.8486 (ptpt) REVERT: A 62 ASN cc_start: 0.8614 (m-40) cc_final: 0.8332 (p0) REVERT: A 137 CYS cc_start: 0.9038 (m) cc_final: 0.8745 (m) REVERT: A 251 MET cc_start: 0.9009 (tpt) cc_final: 0.8403 (tpt) REVERT: B 62 ASN cc_start: 0.8697 (m-40) cc_final: 0.8359 (m110) REVERT: B 137 CYS cc_start: 0.9300 (m) cc_final: 0.9090 (m) REVERT: B 158 MET cc_start: 0.8289 (pmm) cc_final: 0.7636 (mpp) REVERT: B 243 MET cc_start: 0.8506 (tmm) cc_final: 0.8302 (tmm) REVERT: B 248 PHE cc_start: 0.9284 (t80) cc_final: 0.8813 (t80) REVERT: C 62 ASN cc_start: 0.8782 (m-40) cc_final: 0.8502 (p0) REVERT: C 68 GLU cc_start: 0.8374 (mt-10) cc_final: 0.8160 (pp20) REVERT: C 137 CYS cc_start: 0.9147 (m) cc_final: 0.8883 (m) REVERT: C 206 GLN cc_start: 0.9173 (mt0) cc_final: 0.8773 (tt0) REVERT: C 251 MET cc_start: 0.8957 (tpt) cc_final: 0.8409 (tpt) outliers start: 1 outliers final: 0 residues processed: 59 average time/residue: 0.1700 time to fit residues: 14.6419 Evaluate side-chains 50 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 1.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 32 optimal weight: 5.9990 chunk 11 optimal weight: 8.9990 chunk 1 optimal weight: 8.9990 chunk 65 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 80 optimal weight: 9.9990 chunk 29 optimal weight: 5.9990 chunk 40 optimal weight: 2.9990 chunk 14 optimal weight: 9.9990 chunk 30 optimal weight: 7.9990 chunk 4 optimal weight: 3.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.039066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2672 r_free = 0.2672 target = 0.033794 restraints weight = 53777.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2714 r_free = 0.2714 target = 0.034882 restraints weight = 30059.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2743 r_free = 0.2743 target = 0.035665 restraints weight = 19171.053| |-----------------------------------------------------------------------------| r_work (final): 0.2742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.5837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 7481 Z= 0.232 Angle : 0.634 7.584 10145 Z= 0.332 Chirality : 0.040 0.163 1158 Planarity : 0.004 0.057 1272 Dihedral : 12.460 109.635 1191 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 13.39 Ramachandran Plot: Outliers : 1.21 % Allowed : 4.61 % Favored : 94.19 % Rotamer: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.67 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.27), residues: 912 helix: 1.25 (0.24), residues: 429 sheet: -0.84 (0.36), residues: 165 loop : 0.16 (0.36), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 294 PHE 0.013 0.002 PHE B 86 TYR 0.010 0.001 TYR C 315 ARG 0.005 0.001 ARG B 96 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 0.907 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 62 ASN cc_start: 0.8581 (m-40) cc_final: 0.8259 (m110) REVERT: A 137 CYS cc_start: 0.9105 (m) cc_final: 0.8785 (m) REVERT: A 251 MET cc_start: 0.9064 (tpt) cc_final: 0.8461 (tpt) REVERT: B 62 ASN cc_start: 0.8723 (m-40) cc_final: 0.8352 (m110) REVERT: B 137 CYS cc_start: 0.9302 (m) cc_final: 0.9052 (m) REVERT: B 267 ASN cc_start: 0.8841 (p0) cc_final: 0.8518 (p0) REVERT: C 137 CYS cc_start: 0.9177 (m) cc_final: 0.8889 (m) REVERT: C 206 GLN cc_start: 0.9204 (mt0) cc_final: 0.8752 (tt0) REVERT: C 225 THR cc_start: 0.9211 (p) cc_final: 0.8617 (p) REVERT: C 251 MET cc_start: 0.8923 (tpt) cc_final: 0.8398 (tpt) REVERT: C 326 MET cc_start: 0.8530 (tmm) cc_final: 0.8318 (tmm) outliers start: 0 outliers final: 0 residues processed: 56 average time/residue: 0.1671 time to fit residues: 14.1553 Evaluate side-chains 43 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 43 time to evaluate : 0.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 22 optimal weight: 9.9990 chunk 89 optimal weight: 6.9990 chunk 80 optimal weight: 9.9990 chunk 54 optimal weight: 6.9990 chunk 17 optimal weight: 9.9990 chunk 7 optimal weight: 6.9990 chunk 40 optimal weight: 5.9990 chunk 1 optimal weight: 6.9990 chunk 27 optimal weight: 9.9990 chunk 75 optimal weight: 8.9990 chunk 35 optimal weight: 6.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 47 HIS ** B 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 47 HIS ** C 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2810 r_free = 0.2810 target = 0.037342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2612 r_free = 0.2612 target = 0.032245 restraints weight = 55653.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2654 r_free = 0.2654 target = 0.033286 restraints weight = 31103.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2682 r_free = 0.2682 target = 0.034000 restraints weight = 19856.393| |-----------------------------------------------------------------------------| r_work (final): 0.2684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.5981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 7481 Z= 0.408 Angle : 0.756 7.567 10145 Z= 0.395 Chirality : 0.043 0.184 1158 Planarity : 0.004 0.061 1272 Dihedral : 12.840 118.586 1191 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 16.74 Ramachandran Plot: Outliers : 1.21 % Allowed : 5.37 % Favored : 93.42 % Rotamer: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.67 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.27), residues: 912 helix: 0.90 (0.24), residues: 429 sheet: -0.99 (0.36), residues: 159 loop : -0.12 (0.36), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS A 294 PHE 0.024 0.002 PHE C 195 TYR 0.010 0.001 TYR C 191 ARG 0.008 0.001 ARG B 96 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 49 time to evaluate : 0.808 Fit side-chains REVERT: A 62 ASN cc_start: 0.8564 (m-40) cc_final: 0.8210 (m110) REVERT: A 137 CYS cc_start: 0.9023 (m) cc_final: 0.8691 (m) REVERT: A 251 MET cc_start: 0.8993 (tpt) cc_final: 0.8395 (tpt) REVERT: B 62 ASN cc_start: 0.8758 (m-40) cc_final: 0.8465 (m110) REVERT: B 137 CYS cc_start: 0.9276 (m) cc_final: 0.9019 (m) REVERT: B 243 MET cc_start: 0.8469 (tmm) cc_final: 0.8133 (tmm) REVERT: B 267 ASN cc_start: 0.8945 (p0) cc_final: 0.8736 (p0) REVERT: C 62 ASN cc_start: 0.8911 (m-40) cc_final: 0.8588 (p0) REVERT: C 137 CYS cc_start: 0.9207 (m) cc_final: 0.8939 (m) REVERT: C 251 MET cc_start: 0.8941 (tpt) cc_final: 0.8460 (tpt) outliers start: 0 outliers final: 0 residues processed: 49 average time/residue: 0.1802 time to fit residues: 12.9497 Evaluate side-chains 42 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 42 optimal weight: 0.6980 chunk 49 optimal weight: 8.9990 chunk 39 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 77 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 52 optimal weight: 0.9990 chunk 60 optimal weight: 10.0000 chunk 51 optimal weight: 4.9990 chunk 89 optimal weight: 2.9990 chunk 12 optimal weight: 0.9980 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 47 HIS ** A 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 199 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.039625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2686 r_free = 0.2686 target = 0.034264 restraints weight = 52196.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2727 r_free = 0.2727 target = 0.035359 restraints weight = 29291.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2755 r_free = 0.2755 target = 0.036126 restraints weight = 18739.973| |-----------------------------------------------------------------------------| r_work (final): 0.2759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.6383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 7481 Z= 0.173 Angle : 0.646 7.982 10145 Z= 0.329 Chirality : 0.040 0.182 1158 Planarity : 0.004 0.071 1272 Dihedral : 12.204 106.293 1191 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 12.70 Ramachandran Plot: Outliers : 1.21 % Allowed : 3.95 % Favored : 94.85 % Rotamer: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.67 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.28), residues: 912 helix: 1.37 (0.24), residues: 429 sheet: -0.90 (0.36), residues: 165 loop : 0.30 (0.37), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 138 PHE 0.013 0.001 PHE B 86 TYR 0.013 0.001 TYR C 216 ARG 0.005 0.001 ARG B 96 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 0.832 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 137 CYS cc_start: 0.9263 (m) cc_final: 0.8999 (m) REVERT: A 251 MET cc_start: 0.9032 (tpt) cc_final: 0.8353 (tpt) REVERT: B 137 CYS cc_start: 0.9243 (m) cc_final: 0.9020 (m) REVERT: B 243 MET cc_start: 0.8378 (tmm) cc_final: 0.8117 (tmm) REVERT: B 267 ASN cc_start: 0.8791 (p0) cc_final: 0.8523 (p0) REVERT: C 62 ASN cc_start: 0.8929 (m-40) cc_final: 0.8700 (p0) REVERT: C 137 CYS cc_start: 0.9217 (m) cc_final: 0.8955 (m) REVERT: C 206 GLN cc_start: 0.9224 (mt0) cc_final: 0.8773 (tt0) REVERT: C 251 MET cc_start: 0.8980 (tpt) cc_final: 0.8450 (tpt) outliers start: 0 outliers final: 0 residues processed: 55 average time/residue: 0.1808 time to fit residues: 14.5006 Evaluate side-chains 44 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 44 time to evaluate : 0.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 78 optimal weight: 0.7980 chunk 36 optimal weight: 2.9990 chunk 60 optimal weight: 10.0000 chunk 62 optimal weight: 9.9990 chunk 24 optimal weight: 7.9990 chunk 32 optimal weight: 9.9990 chunk 15 optimal weight: 10.0000 chunk 87 optimal weight: 4.9990 chunk 59 optimal weight: 5.9990 chunk 10 optimal weight: 4.9990 chunk 22 optimal weight: 10.0000 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 93 HIS ** B 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 196 ASN ** C 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2853 r_free = 0.2853 target = 0.038745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2651 r_free = 0.2651 target = 0.033399 restraints weight = 53696.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2693 r_free = 0.2693 target = 0.034484 restraints weight = 30096.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2721 r_free = 0.2721 target = 0.035220 restraints weight = 19244.886| |-----------------------------------------------------------------------------| r_work (final): 0.2724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.6446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 7481 Z= 0.266 Angle : 0.687 7.657 10145 Z= 0.347 Chirality : 0.041 0.170 1158 Planarity : 0.004 0.061 1272 Dihedral : 12.242 107.620 1191 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 12.91 Ramachandran Plot: Outliers : 1.10 % Allowed : 4.50 % Favored : 94.41 % Rotamer: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.67 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.28), residues: 912 helix: 1.25 (0.24), residues: 429 sheet: -0.45 (0.40), residues: 141 loop : 0.01 (0.35), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 294 PHE 0.024 0.002 PHE C 86 TYR 0.015 0.001 TYR C 216 ARG 0.005 0.001 ARG C 96 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 53 time to evaluate : 0.863 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 137 CYS cc_start: 0.9169 (m) cc_final: 0.8892 (m) REVERT: A 251 MET cc_start: 0.8979 (tpt) cc_final: 0.8372 (tpt) REVERT: B 62 ASN cc_start: 0.8627 (m-40) cc_final: 0.8232 (m110) REVERT: B 137 CYS cc_start: 0.9225 (m) cc_final: 0.9000 (m) REVERT: B 243 MET cc_start: 0.8410 (tmm) cc_final: 0.8153 (tmm) REVERT: B 267 ASN cc_start: 0.8722 (p0) cc_final: 0.8406 (p0) REVERT: C 62 ASN cc_start: 0.8817 (m-40) cc_final: 0.8531 (p0) REVERT: C 137 CYS cc_start: 0.9196 (m) cc_final: 0.8941 (m) REVERT: C 251 MET cc_start: 0.8954 (tpt) cc_final: 0.8443 (tpt) outliers start: 0 outliers final: 0 residues processed: 53 average time/residue: 0.1833 time to fit residues: 14.2842 Evaluate side-chains 43 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 43 time to evaluate : 0.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 71 optimal weight: 6.9990 chunk 85 optimal weight: 5.9990 chunk 87 optimal weight: 10.0000 chunk 28 optimal weight: 1.9990 chunk 54 optimal weight: 5.9990 chunk 40 optimal weight: 10.0000 chunk 17 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 21 optimal weight: 9.9990 chunk 59 optimal weight: 5.9990 chunk 47 optimal weight: 7.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 268 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2827 r_free = 0.2827 target = 0.037885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2629 r_free = 0.2629 target = 0.032729 restraints weight = 55120.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2671 r_free = 0.2671 target = 0.033808 restraints weight = 30778.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2700 r_free = 0.2700 target = 0.034550 restraints weight = 19562.279| |-----------------------------------------------------------------------------| r_work (final): 0.2703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.6447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.027 7481 Z= 0.330 Angle : 0.715 7.833 10145 Z= 0.366 Chirality : 0.041 0.180 1158 Planarity : 0.006 0.102 1272 Dihedral : 12.283 108.209 1191 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 13.80 Ramachandran Plot: Outliers : 0.88 % Allowed : 5.48 % Favored : 93.64 % Rotamer: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.67 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.27), residues: 912 helix: 1.13 (0.24), residues: 420 sheet: -0.47 (0.41), residues: 138 loop : -0.26 (0.34), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 294 PHE 0.020 0.002 PHE C 86 TYR 0.013 0.001 TYR C 216 ARG 0.004 0.001 ARG B 167 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 0.850 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 137 CYS cc_start: 0.9168 (m) cc_final: 0.8890 (m) REVERT: A 251 MET cc_start: 0.8954 (tpt) cc_final: 0.8379 (tpt) REVERT: B 62 ASN cc_start: 0.8649 (m-40) cc_final: 0.8324 (m110) REVERT: B 137 CYS cc_start: 0.9223 (m) cc_final: 0.8992 (m) REVERT: B 243 MET cc_start: 0.8451 (tmm) cc_final: 0.8162 (tmm) REVERT: B 267 ASN cc_start: 0.8784 (p0) cc_final: 0.8487 (p0) REVERT: C 62 ASN cc_start: 0.8933 (m-40) cc_final: 0.8690 (p0) REVERT: C 137 CYS cc_start: 0.9186 (m) cc_final: 0.8919 (m) REVERT: C 251 MET cc_start: 0.8964 (tpt) cc_final: 0.8453 (tpt) outliers start: 0 outliers final: 0 residues processed: 50 average time/residue: 0.1870 time to fit residues: 14.3554 Evaluate side-chains 41 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 41 time to evaluate : 0.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 20 optimal weight: 7.9990 chunk 52 optimal weight: 2.9990 chunk 58 optimal weight: 7.9990 chunk 31 optimal weight: 8.9990 chunk 41 optimal weight: 3.9990 chunk 56 optimal weight: 4.9990 chunk 10 optimal weight: 1.9990 chunk 19 optimal weight: 8.9990 chunk 59 optimal weight: 0.4980 chunk 43 optimal weight: 9.9990 chunk 36 optimal weight: 3.9990 overall best weight: 2.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.039047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2663 r_free = 0.2663 target = 0.033756 restraints weight = 53981.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2704 r_free = 0.2704 target = 0.034840 restraints weight = 30200.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2733 r_free = 0.2733 target = 0.035610 restraints weight = 19348.057| |-----------------------------------------------------------------------------| r_work (final): 0.2732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.6653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 7481 Z= 0.214 Angle : 0.663 8.828 10145 Z= 0.336 Chirality : 0.040 0.172 1158 Planarity : 0.005 0.072 1272 Dihedral : 12.065 105.706 1191 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 12.64 Ramachandran Plot: Outliers : 0.88 % Allowed : 4.17 % Favored : 94.96 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.67 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.28), residues: 912 helix: 1.22 (0.24), residues: 429 sheet: -0.57 (0.42), residues: 141 loop : -0.15 (0.35), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 244 PHE 0.025 0.002 PHE C 86 TYR 0.013 0.001 TYR C 216 ARG 0.003 0.000 ARG A 130 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 53 time to evaluate : 0.886 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 LEU cc_start: 0.8923 (mt) cc_final: 0.8647 (pp) REVERT: A 137 CYS cc_start: 0.9211 (m) cc_final: 0.8937 (m) REVERT: A 251 MET cc_start: 0.8926 (tpt) cc_final: 0.8316 (tpt) REVERT: B 52 VAL cc_start: 0.9341 (t) cc_final: 0.9057 (p) REVERT: B 137 CYS cc_start: 0.9241 (m) cc_final: 0.8987 (m) REVERT: B 243 MET cc_start: 0.8338 (tmm) cc_final: 0.8078 (tmm) REVERT: B 267 ASN cc_start: 0.8736 (p0) cc_final: 0.8442 (p0) REVERT: C 62 ASN cc_start: 0.8810 (m-40) cc_final: 0.8518 (p0) REVERT: C 137 CYS cc_start: 0.9148 (m) cc_final: 0.8888 (m) REVERT: C 251 MET cc_start: 0.8936 (tpt) cc_final: 0.8406 (tpt) outliers start: 0 outliers final: 0 residues processed: 53 average time/residue: 0.1847 time to fit residues: 14.3015 Evaluate side-chains 44 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 44 time to evaluate : 0.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 72 optimal weight: 0.9990 chunk 47 optimal weight: 3.9990 chunk 22 optimal weight: 10.0000 chunk 85 optimal weight: 7.9990 chunk 77 optimal weight: 7.9990 chunk 86 optimal weight: 2.9990 chunk 58 optimal weight: 7.9990 chunk 43 optimal weight: 20.0000 chunk 7 optimal weight: 7.9990 chunk 21 optimal weight: 6.9990 chunk 24 optimal weight: 4.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2848 r_free = 0.2848 target = 0.038598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2654 r_free = 0.2654 target = 0.033444 restraints weight = 53889.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2696 r_free = 0.2696 target = 0.034515 restraints weight = 30416.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2724 r_free = 0.2724 target = 0.035276 restraints weight = 19428.230| |-----------------------------------------------------------------------------| r_work (final): 0.2724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.6665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 7481 Z= 0.267 Angle : 0.675 8.335 10145 Z= 0.344 Chirality : 0.040 0.178 1158 Planarity : 0.005 0.083 1272 Dihedral : 12.050 106.595 1191 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 12.29 Ramachandran Plot: Outliers : 0.88 % Allowed : 5.15 % Favored : 93.97 % Rotamer: Outliers : 0.00 % Allowed : 0.13 % Favored : 99.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.67 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.28), residues: 912 helix: 1.23 (0.24), residues: 420 sheet: -0.54 (0.42), residues: 141 loop : -0.20 (0.34), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 294 PHE 0.025 0.002 PHE B 259 TYR 0.021 0.001 TYR C 216 ARG 0.002 0.001 ARG A 130 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1722.24 seconds wall clock time: 32 minutes 24.97 seconds (1944.97 seconds total)